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Protein

Isocitrate dehydrogenase [NADP], mitochondrial

Gene

IDH2

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Plays a role in intermediary metabolism and energy production. It may tightly associate or interact with the pyruvate dehydrogenase complex.

Catalytic activityi

Isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH.

Cofactori

Mg2+By similarity, Mn2+By similarityNote: Binds 1 Mg2+ or Mn2+ ion per subunit.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei117SubstrateBy similarity1
Binding sitei122NADPBy similarity1
Binding sitei149SubstrateBy similarity1
Binding sitei172SubstrateBy similarity1
Sitei179Critical for catalysisBy similarity1
Sitei251Critical for catalysisBy similarity1
Metal bindingi291Magnesium or manganeseBy similarity1
Binding sitei299NADPBy similarity1
Metal bindingi314Magnesium or manganeseBy similarity1
Binding sitei367NADP; via amide nitrogen and carbonyl oxygenBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi115 – 117NADPBy similarity3
Nucleotide bindingi349 – 354NADPBy similarity6

GO - Molecular functioni

  • isocitrate dehydrogenase (NADP+) activity Source: CACAO
  • magnesium ion binding Source: UniProtKB
  • NAD binding Source: InterPro

GO - Biological processi

Keywordsi

Molecular functionOxidoreductase
Biological processGlyoxylate bypass, Tricarboxylic acid cycle
LigandMagnesium, Manganese, Metal-binding, NADP

Enzyme and pathway databases

BioCyciMetaCyc:HS00021-MONOMER
BRENDAi1.1.1.42 2681
ReactomeiR-HSA-2151201 Transcriptional activation of mitochondrial biogenesis
R-HSA-71403 Citric acid cycle (TCA cycle)
SIGNORiP48735

Names & Taxonomyi

Protein namesi
Recommended name:
Isocitrate dehydrogenase [NADP], mitochondrial (EC:1.1.1.42)
Short name:
IDH
Alternative name(s):
ICD-M
IDP
NADP(+)-specific ICDH
Oxalosuccinate decarboxylase
Gene namesi
Name:IDH2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 15

Organism-specific databases

EuPathDBiHostDB:ENSG00000182054.9
HGNCiHGNC:5383 IDH2
MIMi147650 gene
neXtProtiNX_P48735

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Mitochondrion

Pathology & Biotechi

Involvement in diseasei

D-2-hydroxyglutaric aciduria 2 (D2HGA2)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA neurometabolic disorder causing developmental delay, epilepsy, hypotonia, and dysmorphic features. Both a mild and a severe phenotype exist. The severe phenotype is homogeneous and is characterized by early infantile-onset epileptic encephalopathy and cardiomyopathy. The mild phenotype has a more variable clinical presentation. Diagnosis is based on the presence of an excess of D-2-hydroxyglutaric acid in the urine.
See also OMIM:613657
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_065174140R → G in D2HGA2. 1 PublicationCorresponds to variant dbSNP:rs267606870Ensembl.1
Natural variantiVAR_065175140R → Q in D2HGA2. 1 PublicationCorresponds to variant dbSNP:rs121913502EnsemblClinVar.1
Glioma (GLM)2 Publications
The gene represented in this entry is involved in disease pathogenesis.
Disease descriptionGliomas are benign or malignant central nervous system neoplasms derived from glial cells. They comprise astrocytomas and glioblastoma multiforme that are derived from astrocytes, oligodendrogliomas derived from oligodendrocytes and ependymomas derived from ependymocytes.
See also OMIM:137800
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_073181158P → L in GLM; somatic mutation. 1 Publication1
Natural variantiVAR_073182162P → S in GLM; somatic mutation. 1 Publication1
Natural variantiVAR_073183172R → G in GLM; somatic mutation; reduces enzymatic activity. 1 PublicationCorresponds to variant dbSNP:rs1057519906Ensembl.1
Natural variantiVAR_073184172R → K in GLM; somatic mutation; reduces enzymatic activity. 2 PublicationsCorresponds to variant dbSNP:rs121913503Ensembl.1
Natural variantiVAR_073185172R → M in GLM; somatic mutation; reduces enzymatic activity. 1 Publication1
enetic variations are associated with cartilaginous tumors such as enchondroma or chondrosarcoma.1 Publication

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi413K → A: 44-fold loss in activity. 1 Publication1
Mutagenesisi413K → Q: 20-fold decrease in Vmax. 1 Publication1
Mutagenesisi413K → R: No appreciable difference in Km for isocitrate and NADP. 1 Publication1

Keywords - Diseasei

Disease mutation

Organism-specific databases

DisGeNETi3418
MalaCardsiIDH2
MIMi137800 phenotype
613657 phenotype
OpenTargetsiENSG00000182054
Orphaneti251589 Anaplastic astrocytoma
251663 Anaplastic oligoastrocytoma
251630 Anaplastic oligodendroglioma
79315 D-2-hydroxyglutaric aciduria
296 Enchondromatosis
251601 Fibrillary astrocytoma
251604 Gemistocytic astrocytoma
163634 Maffucci syndrome
251656 Oligoastrocytoma
251627 Oligodendroglioma
251598 Protoplasmic astrocytoma
PharmGKBiPA29631

Chemistry databases

ChEMBLiCHEMBL3991501
DrugBankiDB01727 Isocitric Acid

Polymorphism and mutation databases

BioMutaiIDH2
DMDMi20141568

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transit peptidei1 – 39MitochondrionBy similarityAdd BLAST39
ChainiPRO_000001442040 – 452Isocitrate dehydrogenase [NADP], mitochondrialAdd BLAST413

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei45N6-acetyllysineBy similarity1
Modified residuei48N6-acetyllysineBy similarity1
Modified residuei67N6-acetyllysineCombined sources1
Modified residuei69N6-acetyllysineBy similarity1
Modified residuei80N6-acetyllysine; alternateBy similarity1
Modified residuei80N6-succinyllysine; alternateBy similarity1
Modified residuei106N6-acetyllysine; alternateCombined sources1
Modified residuei106N6-succinyllysine; alternateBy similarity1
Modified residuei155N6-acetyllysineCombined sources1
Modified residuei166N6-acetyllysine; alternateCombined sources1
Modified residuei166N6-succinyllysine; alternateBy similarity1
Modified residuei180N6-acetyllysine; alternateCombined sources1
Modified residuei180N6-succinyllysine; alternateBy similarity1
Modified residuei193N6-acetyllysine; alternateBy similarity1
Modified residuei193N6-succinyllysine; alternateBy similarity1
Modified residuei199N6-acetyllysineBy similarity1
Modified residuei256N6-acetyllysine; alternateCombined sources1
Modified residuei256N6-succinyllysine; alternateBy similarity1
Modified residuei263N6-acetyllysineCombined sources1
Modified residuei272N6-acetyllysineCombined sources1
Modified residuei275N6-acetyllysineCombined sources1
Modified residuei280N6-acetyllysineBy similarity1
Modified residuei282N6-acetyllysine; alternateCombined sources1
Modified residuei282N6-succinyllysine; alternateBy similarity1
Modified residuei384N6-acetyllysine; alternateBy similarity1
Modified residuei384N6-succinyllysine; alternateBy similarity1
Modified residuei400N6-acetyllysineBy similarity1
Modified residuei413N6-acetyllysine1 Publication1
Modified residuei442N6-acetyllysineCombined sources1

Post-translational modificationi

Acetylation at Lys-413 dramatically reduces catalytic activity. Deacetylated by SIRT3.1 Publication

Keywords - PTMi

Acetylation

Proteomic databases

EPDiP48735
MaxQBiP48735
PaxDbiP48735
PeptideAtlasiP48735
PRIDEiP48735
ProteomicsDBi55932

2D gel databases

OGPiP48735
UCD-2DPAGEiP48735

PTM databases

CarbonylDBiP48735
iPTMnetiP48735
PhosphoSitePlusiP48735
SwissPalmiP48735

Expressioni

Gene expression databases

BgeeiENSG00000182054
CleanExiHS_IDH2
ExpressionAtlasiP48735 baseline and differential
GenevisibleiP48735 HS

Organism-specific databases

HPAiHPA007831

Interactioni

Subunit structurei

Homodimer.

Protein-protein interaction databases

BioGridi109644, 35 interactors
DIPiDIP-61416N
IntActiP48735, 21 interactors
MINTiP48735
STRINGi9606.ENSP00000331897

Chemistry databases

BindingDBiP48735

Structurei

Secondary structure

1452
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi50 – 54Combined sources5
Helixi57 – 69Combined sources13
Turni70 – 74Combined sources5
Beta strandi79 – 83Combined sources5
Helixi86 – 91Combined sources6
Turni92 – 94Combined sources3
Helixi95 – 107Combined sources13
Beta strandi108 – 112Combined sources5
Helixi120 – 126Combined sources7
Helixi135 – 143Combined sources9
Beta strandi146 – 151Combined sources6
Beta strandi169 – 173Combined sources5
Helixi177 – 180Combined sources4
Beta strandi182 – 186Combined sources5
Beta strandi190 – 196Combined sources7
Beta strandi205 – 214Combined sources10
Beta strandi216 – 220Combined sources5
Helixi225 – 242Combined sources18
Beta strandi246 – 250Combined sources5
Turni252 – 254Combined sources3
Helixi258 – 273Combined sources16
Helixi275 – 280Combined sources6
Beta strandi285 – 289Combined sources5
Helixi290 – 299Combined sources10
Beta strandi304 – 308Combined sources5
Helixi310 – 324Combined sources15
Beta strandi329 – 335Combined sources7
Beta strandi342 – 345Combined sources4
Helixi352 – 359Combined sources8
Helixi369 – 386Combined sources18
Helixi389 – 407Combined sources19
Helixi413 – 420Combined sources8
Helixi422 – 424Combined sources3
Turni427 – 429Combined sources3
Helixi434 – 449Combined sources16

3D structure databases

ProteinModelPortaliP48735
SMRiP48735
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni134 – 140Substrate bindingBy similarity7

Sequence similaritiesi

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiKOG1526 Eukaryota
COG0538 LUCA
GeneTreeiENSGT00390000012547
HOGENOMiHOG000019858
HOVERGENiHBG006119
InParanoidiP48735
KOiK00031
OMAiYLNTMDF
OrthoDBiEOG091G06IY
PhylomeDBiP48735
TreeFamiTF300428

Family and domain databases

InterProiView protein in InterPro
IPR019818 IsoCit/isopropylmalate_DH_CS
IPR004790 Isocitrate_DH_NADP
IPR024084 IsoPropMal-DH-like_dom
PANTHERiPTHR11822 PTHR11822, 1 hit
PfamiView protein in Pfam
PF00180 Iso_dh, 1 hit
PIRSFiPIRSF000108 IDH_NADP, 1 hit
SMARTiView protein in SMART
SM01329 Iso_dh, 1 hit
TIGRFAMsiTIGR00127 nadp_idh_euk, 1 hit
PROSITEiView protein in PROSITE
PS00470 IDH_IMDH, 1 hit

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: P48735-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MAGYLRVVRS LCRASGSRPA WAPAALTAPT SQEQPRRHYA DKRIKVAKPV
60 70 80 90 100
VEMDGDEMTR IIWQFIKEKL ILPHVDIQLK YFDLGLPNRD QTDDQVTIDS
110 120 130 140 150
ALATQKYSVA VKCATITPDE ARVEEFKLKK MWKSPNGTIR NILGGTVFRE
160 170 180 190 200
PIICKNIPRL VPGWTKPITI GRHAHGDQYK ATDFVADRAG TFKMVFTPKD
210 220 230 240 250
GSGVKEWEVY NFPAGGVGMG MYNTDESISG FAHSCFQYAI QKKWPLYMST
260 270 280 290 300
KNTILKAYDG RFKDIFQEIF DKHYKTDFDK NKIWYEHRLI DDMVAQVLKS
310 320 330 340 350
SGGFVWACKN YDGDVQSDIL AQGFGSLGLM TSVLVCPDGK TIEAEAAHGT
360 370 380 390 400
VTRHYREHQK GRPTSTNPIA SIFAWTRGLE HRGKLDGNQD LIRFAQMLEK
410 420 430 440 450
VCVETVESGA MTKDLAGCIH GLSNVKLNEH FLNTTDFLDT IKSNLDRALG

RQ
Length:452
Mass (Da):50,909
Last modified:April 3, 2002 - v2
Checksum:i4DDC830AFC06AB52
GO
Isoform 2 (identifier: P48735-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-52: Missing.

Note: No experimental confirmation available.
Show »
Length:400
Mass (Da):45,180
Checksum:iF1274A2EC2243D5E
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti34Q → H in CAA49208 (Ref. 1) Curated1
Sequence conflicti435T → M in CAA49208 (Ref. 1) Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_065174140R → G in D2HGA2. 1 PublicationCorresponds to variant dbSNP:rs267606870Ensembl.1
Natural variantiVAR_065175140R → Q in D2HGA2. 1 PublicationCorresponds to variant dbSNP:rs121913502EnsemblClinVar.1
Natural variantiVAR_073181158P → L in GLM; somatic mutation. 1 Publication1
Natural variantiVAR_073182162P → S in GLM; somatic mutation. 1 Publication1
Natural variantiVAR_073183172R → G in GLM; somatic mutation; reduces enzymatic activity. 1 PublicationCorresponds to variant dbSNP:rs1057519906Ensembl.1
Natural variantiVAR_073184172R → K in GLM; somatic mutation; reduces enzymatic activity. 2 PublicationsCorresponds to variant dbSNP:rs121913503Ensembl.1
Natural variantiVAR_073185172R → M in GLM; somatic mutation; reduces enzymatic activity. 1 Publication1
Natural variantiVAR_076512172R → S Found in patients with cartilagenous tumors. 1 PublicationCorresponds to variant dbSNP:rs1057519736Ensembl.1
Natural variantiVAR_076513172R → T Found in patients with cartilagenous tumors. 1 Publication1
Natural variantiVAR_076514172R → W Found in patients with cartilagenous tumors. 1 Publication1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0562781 – 52Missing in isoform 2. 1 PublicationAdd BLAST52

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X69433 mRNA Translation: CAA49208.1
AK294148 mRNA Translation: BAG57473.1
AK312627 mRNA Translation: BAG35513.1
AK316388 mRNA Translation: BAH14759.1
AC087284 Genomic DNA No translation available.
AC092769 Genomic DNA No translation available.
CH471101 Genomic DNA Translation: EAX02082.1
BC009244 mRNA Translation: AAH09244.1
BC071828 mRNA Translation: AAH71828.1
CCDSiCCDS10359.1 [P48735-1]
CCDS76792.1 [P48735-2]
PIRiS57499
RefSeqiNP_001276839.1, NM_001289910.1 [P48735-2]
NP_001277043.1, NM_001290114.1
NP_002159.2, NM_002168.3 [P48735-1]
UniGeneiHs.596461

Genome annotation databases

EnsembliENST00000330062; ENSP00000331897; ENSG00000182054 [P48735-1]
ENST00000540499; ENSP00000446147; ENSG00000182054 [P48735-2]
GeneIDi3418
KEGGihsa:3418
UCSCiuc002box.4 human [P48735-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiIDHP_HUMAN
AccessioniPrimary (citable) accession number: P48735
Secondary accession number(s): B2R6L6, B4DFL2, Q96GT3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: April 3, 2002
Last modified: July 18, 2018
This is version 182 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 15
    Human chromosome 15: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

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